Most of the bay is between 32 and 75 feet (10 and 20 mt) deep. The seabed near Long Beach has experienced considerable subsidence as a result of oil extraction in the Wilmington Field from the 1950s onward. Ironically, this helped the Port of Long Beach surpass the Port of Los Angeles as the leading port in the United States for a time in the 1980s and 1990s, since the deeper seafloor meant that Long Beach could accommodate ships with deeper drafts than could Los Angeles. Dredging operations related to the construction of a gigantic new marine terminal at the Port of Los Angeles have since made both sides of the bay accessible to even the largest existing container ships.

Natural islands in San Pedro Bay include Terminal Island (actually an augmented mudflat), the site of much of Los Angeles' and Long Beach's port facilities, and Mormon Island, the site of an abortive settlement attempt by San Bernardino-based Mormon pioneers in the 1850s. Land reclamation operations by Los Angeles have considerably enlarged Terminal Island, as well as linking Mormon Island to the mainland. Deadman's Island sat at a landmark at the foot of the Bay, but was removed in 1928 as part of the effort to enlarge the harbor.

An 8.5 miles (13.6 kilometers) long breakwater stretches across most of the bay, with two openings to allow ships to enter the port areas behind it. The initial western section of the breakwater, called the San Pedro Breakwater, was constructed between 1899 and 1911 at San Pedro; the Middle breakwater was completed over the next twenty-five years, and the Long Beach breakwater was finished after World War II.

The Long Beach breakwater is the target of controversy within the harbor towns and Greater Los Angelesconservationists community; with various environmental groups, including the Long Beach chapter of the Surfrider Foundation, proposing modifying or removing the breakwater to promote better water flows and a more natural coastal environment at the mouth of the Los Angeles River. This restoration ecology based removal is opposed by waterfront property owners and shippers, who consider that the breakwater provides needed protection from storm damage.[1][2]

A short documentary addressing the issues surrounding the reconfiguration of the Long Beach breakwater is currently in progress. [3]